Meeting the need for an up-to-date and detailed primer on all aspects of the topic, this ready reference reflects the incredible expansion in the application of FRET and its derivative techniques over the past decade, especially in the biological sciences. This wide diversity is equally mirrored in the range of expert contributors. The book itself is clearly subdivided into four major sections. The first provides some background, theory, and key concepts, while the second section focuses on some common FRET techniques and applications, such as in vitro sensing and diagnostics, the determination of protein, peptide and other biological structures, as well as cellular biosensing with genetically encoded fluorescent indicators. The third section looks at recent developments, beginning with the use of fluorescent proteins, followed by a review of FRET usage with semiconductor quantum dots, along with an overview of multistep FRET. The text concludes with a detailed and greatly updated series of supporting tables on FRET pairs and Forster distances, together with some outlook and perspectives on FRET. Written for both the FRET novice and for the seasoned user, this is a must-have resource for office and laboratory shelves.
Preface xv
List of Contributors xix
Part One Background, Theory, and Concepts 1 (268)
1 How I Remember Theodor Forster 3 (6)
Herbert Dreeskamp
2 Remembering Robert Clegg and Elizabeth 9 (14)
Jares-Erijman and Their Contributions to
FRET
Thomas M. Jovin
2.1 Biographical Sketch of Bob Clegg 10 (1)
2.2 Biographical Sketch of Eli 11 (1)
Jares-Erijman
2.3 The Pervasive Influence of Gregorio 12 (1)
Weber
2.4 Contributions by Bob Clegg to FRET 12 (4)
2.5 Contributions by Eli Jares-Erijman to 16 (2)
FRET
2.6 A Final Thought 18 (5)
References 19 (4)
3 Forster Theory 23 (40)
B. Wieb van der Meer
3.1 Introduction 23 (1)
3.2 Pre-Forster 23 (2)
3.3 Bottom Line 25 (1)
3.4 9000-Form, 9-Form, and Practical 26 (2)
Expressions of the R60 Equation
3.5 Overlap Integral 28 (3)
3.6 Zones 31 (2)
3.7 Transfer Mechanisms 33 (1)
3.8 Kappa-Squared Basics 34 (1)
3.9 Ideal Dipole Approximation 35 (1)
3.10 Resonance as an All-or-Nothing Effect 36 (3)
3.11 Details About the All-or-Nothing 39 (2)
Approximation of Resonance
3.12 Classical Theory Completed 41 (1)
3.13 Oscillator Strength-Emission 42 (1)
Spectrum Relation for the Donor
3.14 Oscillator Strength-Absorption 43 (1)
Spectrum Relation for the Acceptor
3.15 Quantum Mechanical Theory 44 (3)
3.16 Transfer in a Random System 47 (1)
3.17 Details for Transfer in a Random 48 (3)
System
3.18 Concentration Depolarization 51 (1)
3.19 FRET Theory 1965--2012 52 (11)
References 59 (4)
4 Optimizing the Orientation Factor 63 (42)
Kappa-Squared for More Accurate FRET
Measurements
B. Wieb van der Meer
Daniel M. van der Meer
Steven S. Vogel
4.1 Two-Thirds or Not Two-Thirds? 63 (2)
4.2 Relevant Questions 65 (1)
4.3 How to Visualize Kappa-Squared? 65 (3)
4.4 Kappa-Squared Can Be Measured in At 68 (2)
Least One Case
4.5 Averaging Regimes 70 (2)
4.6 Dynamic Averaging Regime 72 (4)
4.7 What Is the Most Probable Value for 76 (7)
Kappa-Squared in the Dynamic Regime?
4.8 Optimistic, Conservative, and 83 (2)
Practical Approaches
4.9 Comparison with Experimental Results 85 (5)
4.10 Smart Simulations Are Superior 90 (2)
4.11 Static Kappa-Squared 92 (9)
4.12 Beyond Regimes 101(1)
4.13 Conclusions 102(3)
References 103(2)
5 How to Apply FRET: From Experimental 105(60)
Design to Data Analysis
Niko Hildebrandt
5.1 Introduction: FRET -- More Than a 105(1)
Four-Letter Word!
5.2 FRET: Let's get started! 106(1)
5.3 FRET: The Basic Concept 107(5)
5.4 FRET: Inevitable Mathematics 112(6)
5.4.1 Forster Distance (or Forster 112(1)
Radius)
5.4.2 FRET Efficiency 113(1)
5.4.2.1 Determination by Donor Quenching 113(1)
5.4.2.2 Determination by Acceptor 113(1)
Sensitization
5.4.2.3 Determination by Donor 114(1)
Quenching and Acceptor Sensitization
5.4.2.4 Determination by Donor 115(1)
Photobleaching
5.4.2.5 Determination by Acceptor 115(1)
Photobleaching
5.4.3 FRET with Multiple Donors and/or 116(2)
Acceptors
5.5 FRET: The Experiment 118(21)
5.5.1 The Donor-Acceptor FRET Pair 118(1)
5.5.2 Forster Distance Determination 119(3)
5.5.3 The Main FRET Experiment 122(1)
5.5.3.1 Steady-State FRET Measurements 123(7)
5.5.3.2 Time-Resolved FRET Measurements 130(3)
5.5.3.3 Interpretation of Time-Resolved 133(6)
FRET Data
5.6 FRET beyond Forster 139(16)
5.6.1 Time-Resolved FRET with 140(1)
Lanthanide-Based Donors
5.6.1.1 Terbium to Quantum Dot FRET 141(6)
Using Time-Resolved Donor Quenching and
Acceptor Sensitization Analysis
5.6.2 BRET and CRET 147(1)
5.6.3 Energy Transfer to Metal 148(2)
Nanoparticles (FRET, NSET, DMPET,
NPILM, etc.)
5.6.4 Other Transfer Mechanisms 150(1)
5.6.4.1 Electron Exchange Energy 151(1)
Transfer (Dexter Transfer)
5.6.4.2 Charge Transfer (Marcus Theory) 152(1)
5.6.4.3 Plasmon Coupling 153(1)
5.6.4.4 Singlet Oxygen Diffusion 154(1)
5.7 Summary and Outlook 155(10)
References 156(9)
6 Materials for FRET Analysis: Beyond 165(104)
Traditional Dye-Dye Combinations
Kim E. Sapsford
Bridget Wildt
Angela Mariani
Andrew B. Yeatts
Igor Medintz
6.1 Introduction 165(1)
6.2 Bioconjugation 166(5)
6.3 Organic Materials 171(17)
6.3.1 Ultraviolet, Visible, and 171(2)
Near-Infrared Emitting Dyes
6.3.2 Quencher Molecules 173(2)
6.3.3 Environmentally Sensitive 175(4)
Fluorophores
6.3.4 Dye-Modified 179(1)
Microspheres/Nanomaterials
6.3.5 Dendrimers and Polymer 180(2)
Macromolecules
6.3.6 Photochromic Dyes 182(4)
6.3.7 Carbon Nanomaterials 186(2)
6.4 Biological Materials 188(23)
6.4.1 Natural Fluorophores 188(2)
6.4.2 Nonnatural Amino Acids 190(2)
6.4.3 Green Fluorescent Protein and 192(8)
Derivatives
6.4.4 Light-Harvesting Proteins 200(1)
6.4.5 DNA-Based 201(1)
Macrostructures/Nanotechnology
6.4.6 Enzyme-Generated Bioluminescence 201(8)
6.4.7 Enzyme-Generated Chemiluminescence 209(2)
6.5 Inorganic Materials 211(20)
6.5.1 Luminescent Lanthanide Complexes 212(5)
and Doped Nano-/Microparticles
6.5.2 Luminescent Transition Metal 217(2)
Complexes
6.5.3 Noble Metal Nanomaterials (Gold, 219(3)
Silver, and Copper)
6.5.4 Silicon-Based Materials 222(1)
6.5.5 Semiconductor Nanocrystals 223(8)
6.6 Multi-FRET Systems 231(5)
6.7 Summary and Outlook 236(33)
References 236(33)
Part Two Common FRET Techniques/Applications 269(162)
7 In Vitro FRET Sensing, Diagnostics, and 271(52)
Personalized Medicine
Samantha Spindel
Jessica Granek
Kim E. Sapsford
7.1 Introduction 271(1)
7.2 Small Organic Molecules and Synthetic 272(1)
Organic Polymers
7.3 Carbohydrate--Lipid 273(1)
7.4 The Biotin--Avidin Interaction 273(2)
7.5 Proteins and Peptides 275(7)
7.5.1 Binding Proteins 275(2)
7.5.2 Antigens and Epitope-Based 277(2)
Peptide Sequences
7.5.3 Peptide Sequences for Enzymatic 279(3)
Sensing
7.6 Antibodies 282(5)
7.7 Nucleic Acid (DNA/RNA) 287(12)
7.7.1 Molecular Beacons 288(1)
7.7.2 Polymerase Chain Reaction and FRET 289(1)
7.7.2.1 FRET Hybridization Probes 290(1)
7.7.2.2 TaqMan 291(1)
7.7.2.3 Scorpion Assay 292(2)
7.7.2.4 Others 294(1)
7.7.3 Isothermal Amplification 294(1)
Reactions and FRET
7.7.4 Clinical Applications of Nucleic 295(1)
Acid Detection Using FRET
7.7.4.1 Detection of Pathogens 295(1)
7.7.4.2 Prognostic and Diagnostic 296(2)
Applications
7.7.4.3 Pharmacogenomics and 298(1)
Personalized Medicine
7.8 Aptamers 299(3)
7.9 High-Throughput and Point-of-Care 302(3)
Devices
7.9.1 PoC Technology Advances 302(2)
7.9.2 PoC Material Advances 304(1)
7.10 Conclusions 305(18)
References 305(18)
8 Single-Molecule Applications 323(34)
Thomas Pons
8.1 Introduction 323(1)
8.2 Single-Molecule FRET of Immobilized 324(12)
Molecules
8.2.1 Experimental Setup 324(1)
8.2.1.1 Molecule Immobilization 324(1)
8.2.1.2 Fluorophore Photostability 325(1)
8.2.1.3 Optical Setup 326(1)
8.2.2 Data Analysis 326(3)
8.2.3 Applications 329(5)
8.2.4 Analyzing Complex FRET 334(2)
Trajectories
8.3 Single-Molecule FRET of Freely 336(10)
Diffusing Molecules
8.3.1 Experimental Setup 336(1)
8.3.2 Applications 337(6)
8.3.3 Advanced Solution smFRET Methods 343(1)
8.3.3.1 Alternate Laser Excitation 343(1)
8.3.3.2 Multiparameter Fluorescence 344(2)
Detection
8.4 Single-Molecule FRET Studies 346(5)
Involving Multiple FRET Partners
8.4.1 Multistep FRET 347(1)
8.4.2 Multi-Acceptor and Multi-Donor 348(3)
Systems
8.5 Conclusions and Perspectives 351(6)
References 353(4)
9 Implementation of FRET Technologies for 357(40)
Studying the Folding and Conformational
Changes in Biological Structures
Philip J. Robinson
Cheryl A. Woolhead
9.1 Introduction to Using FRET in 357(1)
Biological Systems
9.2 Forster Formalism in the 358(2)
Determination of Biological Structures
9.3 FRET Experiments in Complex 360(2)
Biological Systems
9.3.1 The Importance of Experimental 360(1)
Design
9.3.2 Site-Specific Labeling and 361(1)
Choosing the Most Effective FRET Pair
9.4 Biological Model System 1: The 362(3)
Ribosome
9.4.1 Intersubunit Rotation within the 363(2)
Ribosome
9.4.2 Dynamic Intrasubunit Movement 365(1)
Within the Ribosome
9.5 Biological System 2: Nascent 365(3)
Polypeptide Structure
9.6 Biological System 3: 368(3)
Chaperone-Mediated Protein Folding
9.6.1 Signal Recognition Particle 368(1)
9.6.2 Trigger Factor 369(2)
9.7 Biological System 4: Mature Protein 371(4)
Folding Intermediates
9.7.1 Unfolding Kinetics of Monellin 372(2)
9.7.2 Intermediate Folding State of the 374(1)
Src Homology 3 Domain
9.8 Biological System 5: Intersubunit 375(3)
Distance in Multimeric Protein Complexes
9.9 Biological System 6: Protein-Protein 378(7)
Interactions in the Assembly of Protein
Polymers
9.9.1 FtsZ Assembly and Subunit Exchange 379(1)
9.9.2 Defining the Molecular Link in 380(5)
Serpin Polymers
9.10 Biological System 7: FRET in Nucleic 385(12)
Acid Systems
9.10.1 Determining the Structure and 386(2)
Configuration of DNA Junctions
9.10.2 Measuring the Opening and 388(2)
Closing of a Nanoscale DNA Box
9.10.3 FRET Between a DNA Polymerase 390(2)
and Its Substrate
References 392(5)
10 FRET-Based Cellular Sensing with 397(34)
Genetically Encoded Fluorescent Indicators
Jonathan C. Claussen
Niko Hildebrandt
Igor Medintz
10.1 Introduction 397(2)
10.2 Enzymes 399(8)
10.2.1 Kinase Activity/Phosphorylation 399(4)
10.2.2 Protease Activity 403(4)
10.3 Metabolites 407(5)
10.3.1 Sugars 407(3)
10.3.2 Glutamate 410(2)
10.4 Second Messengers 412(9)
10.4.1 cAMP 412(3)
10.4.2 cGMP 415(2)
10.4.3 Nitric Oxide 417(2)
10.4.4 Calcium 419(2)
10.5 Conclusions 421(10)
References 423(8)
Part Three FRET with Recently Developed 431(224)
Materials
11 FRET with Fluorescent Proteins 433(42)
Hiofan Hoi
Yidan Ding
Robert E. Campbell
11.1 Introduction to FPs 433(13)
11.1.1 Wild-Type FPs 433(1)
11.1.1.1 Natural Sources 433(1)
11.1.1.2 Structure 434(2)
11.1.1.3 Chromophore Formation 436(2)
11.1.2 Engineered FPs for FRET 438(1)
Applications
11.1.2.1 Overview 438(2)
11.1.2.2 Blue-Green FRET Pairs 440(1)
11.1.2.3 Cyan-Yellow FRET Pairs 441(2)
11.1.2.4 FRET with Orange, Red, and 443(2)
Far-Red FPs
11.1.2.5 Atypical FPs Useful for FRET 445(1)
Applications
11.1.3 Why Use FPs for FRET? 446(1)
11.2 Using FPs for FRET Imaging 446(16)
11.2.1 Photophysical Properties and 446(1)
Typical Forster Radii
11.2.1.1 Overview 446(1)
11.2.1.2 Spectral Overlap 447(2)
11.2.1.3 Orientation Factors 449(1)
11.2.2 Potential Sources of Artifacts 450(1)
During FRET Imaging
11.2.2.1 Photobleaching 450(1)
11.2.2.2 Photoconversion 451(1)
11.2.2.3 pH Dependence 452(1)
11.2.3 Biochemical and Structural 453(1)
Considerations
11.2.3.1 General Considerations when 453(1)
Labeling Proteins with FPs
11.2.3.2 Labeling Proteins for 454(1)
Intermolecular FRET Experiments
11.2.3.3 Labeling Proteins for 454(1)
Intramolecular FRET Experiments
11.2.3.4 FP Oligomerization and FRET 455(3)
Efficiency
11.2.4 Applications and Examples 458(1)
11.2.4.1 Overview 458(1)
11.2.4.2 FRET Biosensor Case Study 459(1)
11.2.4.3 FRET between FPs and Other 460(2)
Donor or Acceptor Materials
11.3 Conclusions 462(13)
References 463(12)
12 Semiconductor Quantum Dots and FRET 475(132)
W. Russ Algar
Melissa Massey
Ulrich J. Krull
12.1 Introduction 475(1)
12.2 A Quick Review of FRET 476(1)
12.3 Quantum Dots 477(22)
12.3.1 A Brief History 478(1)
12.3.2 The Structure of Quantum Dots: 478(2)
The Core
12.3.3 The Optical Properties of 480(2)
Quantum Dots
12.3.4 Overcoming the Limitations of 482(1)
Molecular Fluorophores
12.3.5 The Structure of Quantum Dots: 483(2)
The Shell
12.3.6 Quantum Confinement 485(3)
12.3.7 Quantum Dot Photophysics 488(3)
12.3.8 Quantum Dot Synthesis 491(2)
12.3.9 Quantum Dot Coatings 493(3)
12.3.10 Quantum Dot Bioconjugation 496(3)
12.3.11 Quantum Dot Nomenclature in 499(1)
This Chapter
12.4 Quantum Dots and FRET 499(9)
12.4.1 Quantum Dots as Donors 499(3)
12.4.2 Applicability of the Forster 502(2)
Formalism
12.4.3 QDs as Acceptors 504(2)
12.4.4 The Importance of Bioconjugate 506(2)
Chemistry
12.5 Quantum Dots as Donors in Biological 508(44)
Applications
12.5.1 Association and Dissociation to 508(1)
Modulate QD-FRET
12.5.1.1 Bioanalysis of Carbohydrates 509(1)
12.5.1.2 Homogeneous Immunoassays 510(1)
12.5.1.3 Hybridization Assays 511(5)
12.5.1.4 Bioanalyses Using Aptamers and 516(3)
DNAzymes
12.5.1.5 Bioanalysis of Hydrolytic 519(5)
Enzymes
12.5.1.6 Gene Delivery 524(1)
12.5.2 Changes in Distance to Modulate 524(4)
QD-FRET
12.5.3 Conformational Insights from 528(2)
QD-FRET
12.5.4 Dynamic Modulation of the 530(4)
Spectral Overlap Integral and QD-FRET
12.5.5 Single-Pair QD-FRET 534(6)
12.5.6 Solid-Phase QD-FRET 540(2)
12.5.6.1 Biomolecular Surface Tethers 542(2)
12.5.6.2 Chemical Conjugation to an 544(1)
Interface
12.5.6.3 Interfacial Ligand Exchange 545(2)
12.5.6.4 Electrostatic Immobilization 547(1)
12.5.6.5 Advantages of Immobilized QDs 548(1)
12.5.7 Photodynamic Therapy 549(3)
12.6 Quantum Dots as Acceptors in 552(17)
Biological Applications
12.6.1 Chemiluminescence Resonance 553(2)
Energy Transfer (CRET)
12.6.2 Bioluminescence Resonance Energy 555(5)
Transfer (BRET)
12.6.3 Lanthanide Donors 560(5)
12.6.4 Quantum Dot Donors (for Quantum 565(4)
Dot Acceptors)
12.7 Energy Transfer between Quantum Dots 569(9)
and Other Nanomaterials
12.7.1 Gold Nanoparticles 569(6)
12.7.2 Carbon Nanomaterials 575(1)
12.7.2.1 Graphene and Graphene Oxide 575(2)
12.7.2.2 Carbon Nanotubes 577(1)
12.8 Nonbiological Applications of 578(5)
Quantum Dots and FRET
12.8.1 Photovoltaic Cells 580(2)
12.8.2 Light-Emitting Diodes (LEDs) 582(1)
12.9 Summary 583(24)
References 584(23)
13 Multistep FRET and Nanotechnology 607(48)
Bo Albinsson
Jonas K. Hannestad
13.1 Introduction 607(1)
13.2 Fundamentals of Multistep FRET 608(7)
13.2.1 Hetero-FRET 609(2)
13.2.2 Multicolor FRET and 611(1)
Alternating-Laser Excitation
13.2.3 Homo-FRET 612(3)
13.3 Energy Transfer in Photosynthesis 615(2)
13.4 Photonic Wires and Multistep FRET in 617(30)
Nanotechnology
13.4.1 Photonic Wires 617(11)
13.4.2 Beyond Wires 628(4)
13.4.3 Light Harvesting 632(6)
13.4.4 Functional Control 638(3)
13.4.5 Quantum Dots in Multistep FRET 641(2)
13.4.6 Potential Outputs and Uses for 643(4)
Channeled Excitation Energy
13.5 Summary 647(1)
13.6 Note Added in Proof 648(7)
References 648(7)
Part Four Supporting Information and 655(112)
Conclusions
14 Data 657(100)
Alice C. Byrne
Matthew M. Byrne
George Coker
Kelly B. Gemmill
Christopher Spillmann
Igor Medintz
Seth L. Sloan
B. Wieb van der Meer
14.1 Tables before 1987 658(1)
14.2 Introduction to the Table of 658(45)
Traditional Chromophores
14.3 Forster Distances and Other FRET 703(1)
Data before 1994
14.4 Forster Distances for Traditional 703(1)
Probes More Recent Than 1993
14.5 FRET Data on Fluorescent Proteins 703(39)
14.6 FRET Data on Quantum Dots 742(1)
14.7 Donor--Acceptor Pairs with a Forster 742(2)
Distance in a Given Range
14.8 Table--Reference Directory 744(13)
References 745(12)
15 Outlook on FRET: The Future of Resonance 757(10)
Energy Transfer
15.1 A Rosy Crystal Ball View of FRET 757(1)
Thomas M. Jovin
15.2 Do Not Ask What FRET Can Do for You, 757(1)
Ask What You Can Do for FRET
B. Wieb van der Meer
15.3 FRET: Future Research with an 758(2)
Exciting Technology
Niko Hildebrandt
15.4 Future of FRET 760(1)
Kim E. Sapsford
15.5 Outlook on Single-Molecule FRET 760(1)
Thomas Pons
15.6 Outlook on FRET with fluorescent 761(1)
proteins
Robert E. Campbell
15.7 Luminescent Nanoparticles: Scaffolds 762(5)
for Assembling "Smarter" FRET Probes
W. Russ Algar
References 764(3)
Index 767
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